X-Git-Url: http://biod.pnpi.spb.ru/gitweb/?a=blobdiff_plain;f=src%2Fgromacs%2Ftrajectoryanalysis%2Fmodules%2Frdf.cpp;h=a8d9b3bd39f6f163a3fefb8e20e693527dd505cc;hb=86f86f19d985cd5516b5f8bd5d3dab4760d4b573;hp=5a11f9f369cac49adf60ad2270f1135ac5803eee;hpb=bd8ff104f5c56e7040041a456a349dac48bf60d9;p=alexxy%2Fgromacs.git

diff --git a/src/gromacs/trajectoryanalysis/modules/rdf.cpp b/src/gromacs/trajectoryanalysis/modules/rdf.cpp
index 5a11f9f369..a8d9b3bd39 100644
--- a/src/gromacs/trajectoryanalysis/modules/rdf.cpp
+++ b/src/gromacs/trajectoryanalysis/modules/rdf.cpp
@@ -62,7 +62,6 @@
 #include "gromacs/options/basicoptions.h"
 #include "gromacs/options/filenameoption.h"
 #include "gromacs/options/ioptionscontainer.h"
-#include "gromacs/options/options.h"
 #include "gromacs/pbcutil/pbc.h"
 #include "gromacs/selection/nbsearch.h"
 #include "gromacs/selection/selection.h"
@@ -99,8 +98,7 @@ class Rdf : public TrajectoryAnalysisModule
 
         virtual void initOptions(IOptionsContainer          *options,
                                  TrajectoryAnalysisSettings *settings);
-        virtual void optionsFinished(Options                    *options,
-                                     TrajectoryAnalysisSettings *settings);
+        virtual void optionsFinished(TrajectoryAnalysisSettings *settings);
         virtual void initAnalysis(const TrajectoryAnalysisSettings &settings,
                                   const TopologyInformation        &top);
         virtual void initAfterFirstFrame(const TrajectoryAnalysisSettings &settings,
@@ -172,6 +170,7 @@ class Rdf : public TrajectoryAnalysisModule
         double                                    cutoff_;
         double                                    rmax_;
         bool                                      bNormalize_;
+        bool                                      bNormalizationSet_;
         bool                                      bXY_;
         bool                                      bExclusions_;
 
@@ -188,7 +187,8 @@ Rdf::Rdf()
       pairCounts_(new AnalysisDataSimpleHistogramModule()),
       normAve_(new AnalysisDataAverageModule()),
       binwidth_(0.002), cutoff_(0.0), rmax_(0.0),
-      bNormalize_(true), bXY_(false), bExclusions_(false),
+      bNormalize_(true), bNormalizationSet_(false), bXY_(false),
+      bExclusions_(false),
       cut2_(0.0), rmax2_(0.0), surfaceGroupCount_(0)
 {
     pairDist_.setMultipoint(true);
@@ -253,6 +253,7 @@ Rdf::initOptions(IOptionsContainer *options, TrajectoryAnalysisSettings *setting
     options->addOption(DoubleOption("bin").store(&binwidth_)
                            .description("Bin width (nm)"));
     options->addOption(BooleanOption("norm").store(&bNormalize_)
+                           .storeIsSet(&bNormalizationSet_)
                            .description("Normalize for bin volume and density"));
     options->addOption(BooleanOption("xy").store(&bXY_)
                            .description("Use only the x and y components of the distance"));
@@ -276,13 +277,13 @@ Rdf::initOptions(IOptionsContainer *options, TrajectoryAnalysisSettings *setting
 }
 
 void
-Rdf::optionsFinished(Options *options, TrajectoryAnalysisSettings *settings)
+Rdf::optionsFinished(TrajectoryAnalysisSettings *settings)
 {
     if (surface_ != "no")
     {
         settings->setFlag(TrajectoryAnalysisSettings::efRequireTop);
 
-        if (options->isSet("norm") && bNormalize_)
+        if (bNormalizationSet_ && bNormalize_)
         {
             GMX_THROW(InconsistentInputError("-surf cannot be combined with -norm"));
         }